For example, all my javascripts are packed (http://dean.edwards.name/packer/) and I have a subfolder /public/javascript/source. It would be a disaster if it was merged and sent to everyone in production.

I'd have to agree with José. Making it a default could lead to some really wicked behavior if you're using 3rd party stuff or, e.g., if you create some JavaScript dynamically using a JavascriptsController and/or SASS.